The agency posted the decision this month stating that when a passenger with a disability identifies themselves, the country's airline should, either ban dogs from the flight, or keep them at least five rows away – depending on the aircraft's filtration system.

"For a certain number of people who are animal-allergic, yes, it can be a problem," said Vancouver allergist Dr. Amin Kanini.

Previously the agency has deemed cat allergies to be a disability, but no rulings were issued on dog allergy disabilities.

Passengers will be required to provide evidence of their allergy in order for the airline to accommodate their health issue.

Air Canada previously made a decision to accommodate seeing eye dogs for visually impaired passengers.

The airline has said that if a crossover should happen, the priority will go to whomever booked their flight first.

"The agency found that, as Air Canada does not provide the appropriate accommodation measures. Air Canada's policy/procedure, as it relates to the carriage of dogs in the aircraft in which a person with a disability due to an allergy of dogs is travelling, constitutes an obstacle to the mobility of Mrs. Greenglass and of other persons with a dog allergy disability," said the Canadian Transportation Agency’s statement on the issue.

The agency has given Air Canada until Sept. 16 to finalize how it will accommodate these passengers.

This decision only applies to Air Canada as it is the only airline named in the complaint.

The agency said that it "examines complaints on a case-by-case basis to determine whether people with disabilities encountered an obstacle to their mobility, and whether the obstacle is undue."

Air Canada told CBC News that it could not comment on the issue as it is still under review.

One frustrated Air Canada customer isn't satisfied with how the airline has implemented its policy for cat allergy sufferers to date. The Ottawa woman, who wishes to remain anonymous, is a frequent flyer and did all the required paperwork to create a medical file with the airline that would allow for a "buffer zone" around her seat that is supposed to be cat-free.

She paid her allergy doctor $75 to fill out the Air Canada forms and has always given the required 48 hours' notice before a flight to request the buffer zone. But, on a recent trip, the woman said she was "horrified" to learn that not only was a passenger with a cat seated within the buffer zone, but right next to her.

"My allergy reaction to cats is that I have trouble breathing … it's a really scary process, and to think of that happening at 35,000 feet is really terrifying," she said.

The woman was moved to another seat but complained to Air Canada, asking for an explanation and for more details about what pet owners have to go through to board the plane. Because of her medical file, the woman is not allowed to check in online or tag her own bags or make any changes to her itinerary but she says pet owners don’t face the same inconveniences.

"They treat the pet owners better than those with allergies," she said.

When Air Canada responded to her complaint, the company said it has never guaranteed an animal-free environment and that staff have been asked to "do their best to seat customers with allergies and customers with pets as far away from each other as possible."

"I realize the system for permitting passengers with allergies and passengers with pets is a sensitive one and unfortunately, we cannot guarantee our process will always be seamless. I can only assure you, we do our best to ensure the safety and comfort of all our passengers to the best of our ability," the customer relations representative wrote.

The customer, however, said she doesn't think Air Canada is taking its own policy seriously and that staff aren't properly trained to handle passengers with medical files for allergies.